src/jalview/appletgui/AnnotationColumnChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.HiddenColumns;
  25 import jalview.schemes.AnnotationColourGradient;
  26 import jalview.util.MessageManager;
  27 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.CardLayout;
  31 import java.awt.Checkbox;
  32 import java.awt.Choice;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.Frame;
  36 import java.awt.Panel;
  37 import java.awt.TextField;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.AdjustmentEvent;
  41 import java.awt.event.AdjustmentListener;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.event.MouseListener;
  47 import java.awt.event.TextEvent;
  48 import java.awt.event.TextListener;
  49 import java.util.Iterator;
  50 import java.util.Vector;
  51
  52 //import javax.swing.JPanel;
  53
  54 //import net.miginfocom.swing.MigLayout;
  55
  56 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  57         ActionListener, AdjustmentListener, ItemListener, MouseListener
  58 {
  59
  60   private Choice annotations = new Choice();
  61
  62   private Panel actionPanel = new Panel();
  63
  64   private TitledPanel thresholdPanel = new TitledPanel();
  65
  66   private Panel switchableViewsPanel = new Panel(new CardLayout());
  67
  68   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  69           .getLayout());
  70
  71   private Panel noGraphFilterView = new Panel();
  72
  73   private Panel graphFilterView = new Panel();
  74
  75   private Panel annotationComboBoxPanel = new Panel();
  76
  77   private BorderLayout borderLayout1 = new BorderLayout();
  78
  79   private BorderLayout gBorderLayout = new BorderLayout();
  80
  81   private BorderLayout ngBorderLayout = new BorderLayout();
  82
  83   private Choice threshold = new Choice();
  84
  85   private StructureFilterPanel gStructureFilterPanel;
  86
  87   private StructureFilterPanel ngStructureFilterPanel;
  88
  89   private StructureFilterPanel currentStructureFilterPanel;
  90
  91   private SearchPanel currentSearchPanel;
  92
  93   private SearchPanel gSearchPanel;
  94
  95   private SearchPanel ngSearchPanel;
  96
  97   private FurtherActionPanel currentFurtherActionPanel;
  98
  99   private FurtherActionPanel gFurtherActionPanel;
 100
 101   private FurtherActionPanel ngFurtherActionPanel;
 102
 103   public static final int ACTION_OPTION_SELECT = 1;
 104
 105   public static int ACTION_OPTION_HIDE = 2;
 106
 107   public static String NO_GRAPH_VIEW = "0";
 108
 109   public static String GRAPH_VIEW = "1";
 110
 111   private int actionOption = ACTION_OPTION_SELECT;
 112
 113   private HiddenColumns oldHiddenColumns;
 114
 115   public AnnotationColumnChooser()
 116   {
 117     try
 118     {
 119       jbInit();
 120     } catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123     }
 124   }
 125
 126   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 127   {
 128     super(av, ap);
 129     frame = new Frame();
 130     frame.add(this);
 131     jalview.bin.JalviewLite.addFrame(frame,
 132             MessageManager.getString("label.select_by_annotation"), 520,
 133             215);
 134
 135     slider.addAdjustmentListener(this);
 136     slider.addMouseListener(this);
 137
 138     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 139     if (anns == null)
 140     {
 141       return;
 142     }
 143     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 144     adjusting = true;
 145     Vector<String> list = new Vector<>();
 146     int index = 1;
 147     for (int i = 0; i < anns.length; i++)
 148     {
 149       String label = anns[i].label;
 150       if (anns[i].sequenceRef != null)
 151       {
 152         label = label + "_" + anns[i].sequenceRef.getName();
 153       }
 154       if (!list.contains(label))
 155       {
 156         list.addElement(label);
 157       }
 158       else
 159       {
 160         list.addElement(label + "_" + (index++));
 161       }
 162     }
 163
 164     for (int i = 0; i < list.size(); i++)
 165     {
 166       annotations.addItem(list.elementAt(i).toString());
 167     }
 168
 169     populateThresholdComboBox(threshold);
 170     AnnotationColumnChooser lastChooser = av
 171             .getAnnotationColumnSelectionState();
 172     // restore Object state from the previous session if one exists
 173     if (lastChooser != null)
 174     {
 175       currentSearchPanel = lastChooser
 176               .getCurrentSearchPanel();
 177       currentStructureFilterPanel = lastChooser
 178               .getCurrentStructureFilterPanel();
 179       annotations.select(lastChooser
 180               .getAnnotations().getSelectedIndex());
 181       threshold.select(lastChooser
 182               .getThreshold().getSelectedIndex());
 183       actionOption = lastChooser
 184               .getActionOption();
 185       percentThreshold.setState(lastChooser.percentThreshold.getState());
 186     }
 187
 188     try
 189     {
 190       jbInit();
 191     } catch (Exception ex)
 192     {
 193     }
 194     adjusting = false;
 195
 196     updateView();
 197     frame.invalidate();
 198     frame.pack();
 199   }
 200
 201   private void jbInit() throws Exception
 202   {
 203     ok.setLabel(MessageManager.getString("action.ok"));
 204
 205     cancel.setLabel(MessageManager.getString("action.cancel"));
 206
 207     thresholdValue.setEnabled(false);
 208     thresholdValue.setColumns(7);
 209     thresholdValue.setCaretPosition(0);
 210
 211     ok.addActionListener(this);
 212     cancel.addActionListener(this);
 213     annotations.addItemListener(this);
 214     thresholdValue.addActionListener(this);
 215     threshold.addItemListener(this);
 216
 217     slider.setBackground(Color.white);
 218     slider.setEnabled(false);
 219     slider.setPreferredSize(new Dimension(100, 32));
 220
 221     thresholdPanel.setBackground(Color.white);
 222     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 223     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 224
 225     percentThreshold.setLabel("As percentage");
 226     percentThreshold.addItemListener(this);
 227
 228     actionPanel.setBackground(Color.white);
 229     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 230
 231     graphFilterView.setLayout(gBorderLayout);
 232     graphFilterView.setBackground(Color.white);
 233
 234     noGraphFilterView.setLayout(ngBorderLayout);
 235     noGraphFilterView.setBackground(Color.white);
 236
 237     annotationComboBoxPanel.setBackground(Color.white);
 238     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 239
 240     gSearchPanel = new SearchPanel(this);
 241     ngSearchPanel = new SearchPanel(this);
 242     gFurtherActionPanel = new FurtherActionPanel(this);
 243     ngFurtherActionPanel = new FurtherActionPanel(this);
 244     gStructureFilterPanel = new StructureFilterPanel(this);
 245     ngStructureFilterPanel = new StructureFilterPanel(this);
 246
 247     thresholdPanel.setTitle("Threshold Filter");
 248     thresholdPanel.add(getThreshold());
 249     thresholdPanel.add(slider);
 250     thresholdPanel.add(thresholdValue);
 251     thresholdPanel.add(percentThreshold);
 252
 253     actionPanel.add(ok);
 254     actionPanel.add(cancel);
 255
 256     Panel staticPanel = new Panel();
 257     staticPanel.setLayout(new BorderLayout());
 258     staticPanel.setBackground(Color.white);
 259
 260     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 261     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 262
 263     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 264     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 265     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 266
 267     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 268     noGraphFilterView.add(ngStructureFilterPanel,
 269             java.awt.BorderLayout.CENTER);
 270     noGraphFilterView.add(ngFurtherActionPanel,
 271             java.awt.BorderLayout.CENTER);
 272
 273     annotationComboBoxPanel.add(getAnnotations());
 274     switchableViewsPanel.add(noGraphFilterView,
 275             AnnotationColumnChooser.NO_GRAPH_VIEW);
 276     switchableViewsPanel.add(graphFilterView,
 277             AnnotationColumnChooser.GRAPH_VIEW);
 278
 279     this.setLayout(borderLayout1);
 280     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 281     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 282     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 283
 284     selectedAnnotationChanged();
 285     this.validate();
 286   }
 287
 288   @Override
 289   @SuppressWarnings("unchecked")
 290   public void reset()
 291   {
 292     if (this.getOldHiddenColumns() != null)
 293     {
 294       av.getColumnSelection().clear();
 295
 296       if (av.getAnnotationColumnSelectionState() != null)
 297       {
 298         HiddenColumns oldHidden = av
 299                 .getAnnotationColumnSelectionState()
 300                 .getOldHiddenColumns();
 301         if (oldHidden != null)
 302         {
 303           for (Iterator<int[]> itr = oldHidden.iterator(); itr.hasNext();)
 304           {
 305             int positions[] = itr.next();
 306             av.hideColumns(positions[0], positions[1]);
 307           }
 308         }
 309         av.getAlignment().setHiddenColumns(oldHidden);
 310       }
 311       ap.paintAlignment(true);
 312     }
 313
 314   }
 315
 316   @Override
 317   public void adjustmentValueChanged(AdjustmentEvent evt)
 318   {
 319     if (!adjusting)
 320     {
 321       setThresholdValueText();
 322       valueChanged(!sliderDragging);
 323     }
 324   }
 325
 326   protected void addSliderMouseListeners()
 327   {
 328
 329     slider.addMouseListener(new MouseAdapter()
 330     {
 331       @Override
 332       public void mousePressed(MouseEvent e)
 333       {
 334         sliderDragging = true;
 335         super.mousePressed(e);
 336       }
 337
 338       @Override
 339       public void mouseDragged(MouseEvent e)
 340       {
 341         sliderDragging = true;
 342         super.mouseDragged(e);
 343       }
 344
 345       @Override
 346       public void mouseReleased(MouseEvent evt)
 347       {
 348         if (sliderDragging)
 349         {
 350           sliderDragging = false;
 351           valueChanged(true);
 352         }
 353         ap.paintAlignment(true);
 354       }
 355     });
 356   }
 357
 358   @Override
 359   public void valueChanged(boolean updateAllAnnotation)
 360   {
 361     if (slider.isEnabled())
 362     {
 363       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 364       updateView();
 365       ap.paintAlignment(false);
 366     }
 367   }
 368
 369   public Choice getThreshold()
 370   {
 371     return threshold;
 372   }
 373
 374   public void setThreshold(Choice threshold)
 375   {
 376     this.threshold = threshold;
 377   }
 378
 379   public Choice getAnnotations()
 380   {
 381     return annotations;
 382   }
 383
 384   public void setAnnotations(Choice annotations)
 385   {
 386     this.annotations = annotations;
 387   }
 388
 389   @Override
 390   public void updateView()
 391   {
 392     // Check if combobox is still adjusting
 393     if (adjusting)
 394     {
 395       return;
 396     }
 397
 398     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 399     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 400             .getSelectedIndex()]);
 401
 402     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 403             .getSelectedIndex());
 404
 405     slider.setEnabled(true);
 406     thresholdValue.setEnabled(true);
 407     percentThreshold.setEnabled(true);
 408
 409     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 410     {
 411       slider.setEnabled(false);
 412       thresholdValue.setEnabled(false);
 413       thresholdValue.setText("");
 414       percentThreshold.setEnabled(false);
 415       // build filter params
 416     }
 417     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 418     {
 419       if (getCurrentAnnotation().threshold == null)
 420       {
 421         getCurrentAnnotation()
 422                 .setThreshold(
 423                         new jalview.datamodel.GraphLine(
 424                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 425                                 "Threshold", Color.black));
 426       }
 427
 428       adjusting = true;
 429       float range = getCurrentAnnotation().graphMax * 1000
 430               - getCurrentAnnotation().graphMin * 1000;
 431
 432       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 433       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 434       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 435       setThresholdValueText();
 436       // slider.setMajorTickSpacing((int) (range / 10f));
 437       slider.setEnabled(true);
 438       thresholdValue.setEnabled(true);
 439       percentThreshold.setEnabled(true);
 440       adjusting = false;
 441
 442       // build filter params
 443       filterParams
 444               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 445       if (getCurrentAnnotation().isQuantitative())
 446       {
 447         filterParams
 448                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 449
 450         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 451         {
 452           filterParams
 453                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 454         }
 455         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 456         {
 457           filterParams
 458                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 459         }
 460       }
 461     }
 462
 463     if (currentStructureFilterPanel != null)
 464     {
 465       if (currentStructureFilterPanel.alphaHelix.getState())
 466       {
 467         filterParams.setFilterAlphaHelix(true);
 468       }
 469       if (currentStructureFilterPanel.betaStrand.getState())
 470       {
 471         filterParams.setFilterBetaSheet(true);
 472       }
 473       if (currentStructureFilterPanel.turn.getState())
 474       {
 475         filterParams.setFilterTurn(true);
 476       }
 477     }
 478
 479     if (currentSearchPanel != null)
 480     {
 481
 482       if (!currentSearchPanel.searchBox.getText().isEmpty())
 483       {
 484         currentSearchPanel.description.setEnabled(true);
 485         currentSearchPanel.displayName.setEnabled(true);
 486         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 487         if (currentSearchPanel.displayName.getState())
 488         {
 489           filterParams
 490                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 491         }
 492         if (currentSearchPanel.description.getState())
 493         {
 494           filterParams
 495                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 496         }
 497       }
 498       else
 499       {
 500         currentSearchPanel.description.setEnabled(false);
 501         currentSearchPanel.displayName.setEnabled(false);
 502       }
 503     }
 504
 505     av.getColumnSelection().filterAnnotations(
 506             getCurrentAnnotation().annotations, filterParams);
 507
 508     av.showAllHiddenColumns();
 509     if (getActionOption() == ACTION_OPTION_HIDE)
 510     {
 511       av.hideSelectedColumns();
 512     }
 513
 514     filterParams = null;
 515     av.setAnnotationColumnSelectionState(this);
 516     ap.paintAlignment(true);
 517   }
 518
 519   public HiddenColumns getOldHiddenColumns()
 520   {
 521     return oldHiddenColumns;
 522   }
 523
 524   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 525   {
 526     if (currentHiddenColumns != null)
 527     {
 528       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 529     }
 530   }
 531
 532   public FurtherActionPanel getCurrentFutherActionPanel()
 533   {
 534     return currentFurtherActionPanel;
 535   }
 536
 537   public void setCurrentFutherActionPanel(
 538           FurtherActionPanel currentFutherActionPanel)
 539   {
 540     this.currentFurtherActionPanel = currentFutherActionPanel;
 541   }
 542
 543   public SearchPanel getCurrentSearchPanel()
 544   {
 545     return currentSearchPanel;
 546   }
 547
 548   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 549   {
 550     this.currentSearchPanel = currentSearchPanel;
 551   }
 552
 553   public int getActionOption()
 554   {
 555     return actionOption;
 556   }
 557
 558   public void setActionOption(int actionOption)
 559   {
 560     this.actionOption = actionOption;
 561   }
 562
 563   public StructureFilterPanel getCurrentStructureFilterPanel()
 564   {
 565     return currentStructureFilterPanel;
 566   }
 567
 568   public void setCurrentStructureFilterPanel(
 569           StructureFilterPanel currentStructureFilterPanel)
 570   {
 571     this.currentStructureFilterPanel = currentStructureFilterPanel;
 572   }
 573
 574   @Override
 575   public void itemStateChanged(ItemEvent e)
 576   {
 577     if (e.getSource() == annotations)
 578     {
 579       selectedAnnotationChanged();
 580     }
 581     else if (e.getSource() == threshold)
 582     {
 583       threshold_actionPerformed(null);
 584     }
 585     else if (e.getSource() == percentThreshold)
 586     {
 587       if (!adjusting)
 588       {
 589         percentageValue_actionPerformed();
 590       }
 591
 592     }
 593   }
 594
 595   public void selectedAnnotationChanged()
 596   {
 597     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 598     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 599             .getSelectedIndex()].isQuantitative())
 600     {
 601       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 602     }
 603
 604     gSearchPanel.syncState();
 605     gFurtherActionPanel.syncState();
 606     gStructureFilterPanel.syncState();
 607
 608     ngSearchPanel.syncState();
 609     ngFurtherActionPanel.syncState();
 610     ngStructureFilterPanel.syncState();
 611
 612     switchableViewsLayout.show(switchableViewsPanel, currentView);
 613     updateView();
 614   }
 615
 616   public class FurtherActionPanel extends Panel implements ItemListener
 617   {
 618     private AnnotationColumnChooser aColChooser;
 619
 620     private Choice furtherAction = new Choice();
 621
 622     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 623     {
 624       this.aColChooser = aColChooser;
 625       furtherAction.addItem("Select");
 626       furtherAction.addItem("Hide");
 627       furtherAction.addItemListener(this);
 628       syncState();
 629
 630       // this.setTitle("Filter Actions");
 631       // this.setFont(JvSwingUtils.getLabelFont());
 632
 633       this.add(furtherAction);
 634     }
 635
 636     public void syncState()
 637     {
 638       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 639       {
 640         furtherAction.select("Hide");
 641       }
 642       else
 643       {
 644         furtherAction.select("Select");
 645       }
 646     }
 647
 648     @Override
 649     public void itemStateChanged(ItemEvent e)
 650     {
 651       aColChooser.setCurrentFutherActionPanel(this);
 652       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 653       {
 654         setActionOption(ACTION_OPTION_SELECT);
 655         updateView();
 656       }
 657       else
 658       {
 659         setActionOption(ACTION_OPTION_HIDE);
 660         updateView();
 661       }
 662
 663     }
 664   }
 665
 666   public class StructureFilterPanel extends TitledPanel implements
 667           ItemListener
 668   {
 669     private AnnotationColumnChooser aColChooser;
 670
 671     private Checkbox alphaHelix = new Checkbox();
 672
 673     private Checkbox betaStrand = new Checkbox();
 674
 675     private Checkbox turn = new Checkbox();
 676
 677     private Checkbox all = new Checkbox();
 678
 679     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 680     {
 681       this.aColChooser = aColChooser;
 682
 683       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 684       alphaHelix.setBackground(Color.white);
 685
 686       alphaHelix.addItemListener(this);
 687
 688       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 689       betaStrand.setBackground(Color.white);
 690       betaStrand.addItemListener(this);
 691
 692       turn.setLabel(MessageManager.getString("label.turn"));
 693       turn.setBackground(Color.white);
 694       turn.addItemListener(this);
 695
 696       all.setLabel(MessageManager.getString("label.select_all"));
 697       all.setBackground(Color.white);
 698       all.addItemListener(this);
 699
 700       this.setBackground(Color.white);
 701       this.setTitle("Structure Filter");
 702       // this.setFont(JvSwingUtils.getLabelFont());
 703
 704       this.add(all);
 705       this.add(alphaHelix);
 706       this.add(betaStrand);
 707       this.add(turn);
 708     }
 709
 710     public void alphaHelix_actionPerformed()
 711     {
 712       updateSelectAllState();
 713       aColChooser.setCurrentStructureFilterPanel(this);
 714       aColChooser.updateView();
 715     }
 716
 717     public void betaStrand_actionPerformed()
 718     {
 719       updateSelectAllState();
 720       aColChooser.setCurrentStructureFilterPanel(this);
 721       aColChooser.updateView();
 722     }
 723
 724     public void turn_actionPerformed()
 725     {
 726       updateSelectAllState();
 727       aColChooser.setCurrentStructureFilterPanel(this);
 728       aColChooser.updateView();
 729     }
 730
 731     public void all_actionPerformed()
 732     {
 733       if (all.getState())
 734       {
 735         alphaHelix.setState(true);
 736         betaStrand.setState(true);
 737         turn.setState(true);
 738       }
 739       else
 740       {
 741         alphaHelix.setState(false);
 742         betaStrand.setState(false);
 743         turn.setState(false);
 744       }
 745       aColChooser.setCurrentStructureFilterPanel(this);
 746       aColChooser.updateView();
 747     }
 748
 749     public void updateSelectAllState()
 750     {
 751       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 752       {
 753         all.setState(true);
 754       }
 755       else
 756       {
 757         all.setState(false);
 758       }
 759     }
 760
 761     public void syncState()
 762     {
 763       StructureFilterPanel sfp = aColChooser
 764               .getCurrentStructureFilterPanel();
 765       if (sfp != null)
 766       {
 767         alphaHelix.setState(sfp.alphaHelix.getState());
 768         betaStrand.setState(sfp.betaStrand.getState());
 769         turn.setState(sfp.turn.getState());
 770         if (sfp.all.getState())
 771         {
 772           all.setState(true);
 773           alphaHelix.setState(true);
 774           betaStrand.setState(true);
 775           turn.setState(true);
 776         }
 777       }
 778
 779     }
 780
 781     @Override
 782     public void itemStateChanged(ItemEvent e)
 783     {
 784       if (e.getSource() == alphaHelix)
 785       {
 786         alphaHelix_actionPerformed();
 787       }
 788       else if (e.getSource() == betaStrand)
 789       {
 790         betaStrand_actionPerformed();
 791       }
 792       else if (e.getSource() == turn)
 793       {
 794         turn_actionPerformed();
 795       }
 796       else if (e.getSource() == all)
 797       {
 798         all_actionPerformed();
 799       }
 800     }
 801   }
 802
 803   public class SearchPanel extends TitledPanel implements ItemListener
 804   {
 805     private AnnotationColumnChooser aColChooser;
 806
 807     private Checkbox displayName = new Checkbox();
 808
 809     private Checkbox description = new Checkbox();
 810
 811     private TextField searchBox = new TextField(10);
 812
 813     public SearchPanel(AnnotationColumnChooser aColChooser)
 814     {
 815
 816       this.aColChooser = aColChooser;
 817       searchBox.addTextListener(new TextListener()
 818       {
 819
 820         @Override
 821         public void textValueChanged(TextEvent e)
 822         {
 823           searchStringAction();
 824
 825         }
 826
 827       });
 828
 829       displayName.setLabel(MessageManager.getString("label.label"));
 830       displayName.setEnabled(false);
 831       displayName.addItemListener(this);
 832
 833       description.setLabel(MessageManager.getString("label.description"));
 834       description.setEnabled(false);
 835       description.addItemListener(this);
 836       this.setTitle("Search Filter");
 837       // this.setFont(JvSwingUtils.getLabelFont());
 838
 839       syncState();
 840       this.add(searchBox);
 841       this.add(displayName);
 842       this.add(description);
 843     }
 844
 845     public void displayNameCheckboxAction()
 846     {
 847       aColChooser.setCurrentSearchPanel(this);
 848       aColChooser.updateView();
 849     }
 850
 851     public void discriptionCheckboxAction()
 852     {
 853       aColChooser.setCurrentSearchPanel(this);
 854       aColChooser.updateView();
 855     }
 856
 857     public void searchStringAction()
 858     {
 859       aColChooser.setCurrentSearchPanel(this);
 860       aColChooser.updateView();
 861     }
 862
 863     public void syncState()
 864     {
 865       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 866       if (sp != null)
 867       {
 868         description.setEnabled(sp.description.isEnabled());
 869         description.setState(sp.description.getState());
 870
 871         displayName.setEnabled(sp.displayName.isEnabled());
 872         displayName.setState(sp.displayName.getState());
 873
 874         searchBox.setText(sp.searchBox.getText());
 875       }
 876     }
 877
 878     @Override
 879     public void itemStateChanged(ItemEvent e)
 880     {
 881       if (e.getSource() == displayName)
 882       {
 883         displayNameCheckboxAction();
 884       }
 885       else if (e.getSource() == description)
 886       {
 887         discriptionCheckboxAction();
 888       }
 889
 890     }
 891   }
 892
 893   @Override
 894   public void actionPerformed(ActionEvent evt)
 895   {
 896
 897     if (evt.getSource() == ok)
 898     {
 899       ok_actionPerformed(null);
 900     }
 901     else if (evt.getSource() == cancel)
 902     {
 903       cancel_actionPerformed(null);
 904     }
 905     else if (evt.getSource() == thresholdValue)
 906     {
 907       thresholdValue_actionPerformed(null);
 908     }
 909     else
 910     {
 911       updateView();
 912     }
 913   }
 914
 915   @Override
 916   public void mouseClicked(MouseEvent e)
 917   {
 918     // TODO Auto-generated method stub
 919
 920   }
 921
 922   @Override
 923   public void mousePressed(MouseEvent e)
 924   {
 925     if (e.getSource() == slider)
 926     {
 927       updateView();
 928     }
 929
 930   }
 931
 932   @Override
 933   public void mouseReleased(MouseEvent e)
 934   {
 935     if (e.getSource() == slider)
 936     {
 937       updateView();
 938     }
 939   }
 940
 941   @Override
 942   public void mouseEntered(MouseEvent e)
 943   {
 944     if (e.getSource() == slider)
 945     {
 946       updateView();
 947     }
 948   }
 949
 950   @Override
 951   public void mouseExited(MouseEvent e)
 952   {
 953     if (e.getSource() == slider)
 954     {
 955       updateView();
 956     }
 957   }
 958
 959 }